hii am performing protein ligand binding free energy calculation through alchemical pathway. i made both topologies and generated distance, dihedral and angle restraints. in the index file i defined the restrained atoms. the error i got in energy minimization grompp is that the atom is out of range. it is because my protein is starting from atom num 1 and also my ligand starts with 1. in the gro file the numbering is changed , protein starts with 1 and ends with 1020 , and ligand starts after 1020. but in topology i included the ligand.itp (from acpype) into complex topology file, and both molecules starts with 1. how can i change the numbering of ligand atoms as in gro file. pdb2gmx -renum is not working because it is small ligand not a protein or peptide. if there is any code or any program please suggest. thanks in advance. Sana Saeed Khan,Teaching-Research AssistantChemoinformatics LabGraduate Student, MS bioinfoDepartment of BioinformaticsSoongsil University, Seoul, South Korea.